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CHECK report for CNPBayes on tokay2

This page was generated on 2019-01-10 15:36:06 -0500 (Thu, 10 Jan 2019).

Package 292/1651HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CNPBayes 1.13.5
Jacob Carey
Snapshot Date: 2019-01-09 16:46:14 -0500 (Wed, 09 Jan 2019)
URL: https://git.bioconductor.org/packages/CNPBayes
Branch: master
Last Commit: 1e9cdbb
Last Changed Date: 2019-01-03 09:20:51 -0500 (Thu, 03 Jan 2019)
malbec2 Linux (Ubuntu 18.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: CNPBayes
Version: 1.13.5
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNPBayes.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CNPBayes_1.13.5.tar.gz
StartedAt: 2019-01-10 02:39:03 -0500 (Thu, 10 Jan 2019)
EndedAt: 2019-01-10 03:08:11 -0500 (Thu, 10 Jan 2019)
EllapsedTime: 1748.2 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: CNPBayes.Rcheck
Warnings: 4

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNPBayes.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings CNPBayes_1.13.5.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CNPBayes.Rcheck'
* using R Under development (unstable) (2018-11-18 r75627)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNPBayes/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNPBayes' version '1.13.5'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'CNPBayes' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIFAfHZ/R.INSTALL1f145fdc4500/CNPBayes/man/tile-functions.Rd:28: file link 'ntile' in package 'dplyr' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/CNPBayes.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   2.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'RcppArmadillo'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.simulate_data_multi2: no visible binding for global variable 'id'
augmentData: no visible binding for global variable 'medians'
augmentData: no visible binding for global variable 'nhom'
augmentData: no visible binding for global variable 'id'
augmentData: no visible binding for global variable 'batch_index'
bafLikelihood: no visible binding for global variable 'snpdat'
ci95.wrap: no visible global function definition for 't.test'
combineChains: no visible binding for global variable '.'
combineModels: no visible binding for global variable '.'
combineModels: no visible binding for global variable 'id'
component_stats: no visible binding for global variable 'batches'
component_stats: no visible binding for global variable 'copy_number'
component_stats: no visible binding for global variable 'log_ratio'
find_surrogates: no visible binding for global variable
  'provisional_batch'
gibbs_trios2: no visible binding for global variable 'maplabel'
gibbs_trios2: no visible binding for global variable 'mprob'
gibbs_trios3: no visible binding for global variable 'maplabel'
gibbs_trios3: no visible binding for global variable 'mprob'
gibbs_trios_K2: no visible binding for global variable
  '.gibbs_trios_mcmc2'
gibbs_trios_K3: no visible binding for global variable
  '.gibbs_trios_mcmc3'
longFormatK: no visible binding for global variable '.'
longFormatK: no visible binding for global variable 's'
longFormatKB: no visible binding for global variable '.'
longFormatKB: no visible binding for global variable 's'
longFormatKB: no visible binding for global variable 'bk'
longFormatKB2: no visible binding for global variable '.'
longFormatKB2: no visible binding for global variable 's'
longFormatKB2: no visible binding for global variable 'bk'
modelSpecs: no visible binding for global variable 'model'
mprob.matrix: no visible global function definition for ':='
mprob.matrix: no visible binding for global variable 'parents'
mprob.matrix: no visible binding for global variable 'father'
mprob.matrix: no visible binding for global variable 'mother'
posteriorSimulationPooled: possible error in `mcmcParams<-`(object,
  force = TRUE, value = `*tmpv*`): unused argument (force = TRUE)
predictiveTibble: no visible binding for global variable 'value'
simulate_data_multi2: no visible binding for global variable
  'copy_number'
simulate_data_multi3: no visible binding for global variable
  'copy_number'
startAtTrueValues2: no visible binding for global variable
  'copy_number'
triodata: no visible binding for global variable 'id'
augmentData2,MultiBatchList: no visible binding for global variable
  'model'
augmentData2,MultiBatchList: no visible binding for global variable '.'
augmentData2,MultiBatchList: no visible binding for global variable
  'id'
batch<-,MultiBatch-numeric: no visible global function definition for
  'spec'
batch<-,MultiBatch-numeric: no visible global function definition for
  'spec<-'
coerce,McmcChains-list: no visible binding for global variable 's'
computePrec,MultiBatch: no visible binding for global variable 'prec'
findSurrogates,MultiBatch: no visible binding for global variable 'id'
findSurrogates,MultiBatch: no visible binding for global variable
  'provisional_batch'
findSurrogates,MultiBatch: no visible binding for global variable
  'batch_labels'
sigma,MultiBatchCopyNumberPooled: no visible binding for global
  variable 's2'
Undefined global functions or variables:
  . .gibbs_trios_mcmc2 .gibbs_trios_mcmc3 := batch_index batch_labels
  batches bk copy_number father id log_ratio maplabel medians model
  mother mprob nhom parents prec provisional_batch s s2 snpdat spec
  spec<- t.test value
Consider adding
  importFrom("stats", "t.test")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'TBM' 'findSurrogates' 'modelName' 'p'
Undocumented S4 methods:
  generic '[' and siglist 'MixtureModel,logical,ANY,ANY'
  generic '[' and siglist 'MixtureModel,numeric,ANY,ANY'
  generic '[' and siglist 'MultiBatchList,ANY,ANY,ANY'
  generic '[<-' and siglist 'MultiBatchList,ANY,ANY,ANY'
  generic '[[' and siglist 'MultiBatchList,character,ANY'
  generic '[[' and siglist 'MultiBatchList,numeric,ANY'
  generic '[[<-' and siglist 'MultiBatchList,ANY,ANY'
  generic 'batch' and siglist 'MultiBatch'
  generic 'batch' and siglist 'MultiBatchList'
  generic 'burnin' and siglist 'MultiBatch'
  generic 'burnin' and siglist 'MultiBatchList'
  generic 'burnin<-' and siglist 'MultiBatch,numeric'
  generic 'burnin<-' and siglist 'MultiBatchList,numeric'
  generic 'chains' and siglist 'MultiBatch'
  generic 'chains' and siglist 'MultiBatchList'
  generic 'dfr' and siglist 'MultiBatch'
  generic 'dfr' and siglist 'MultiBatchList'
  generic 'hyperParams' and siglist 'MultiBatch'
  generic 'hyperParams' and siglist 'MultiBatchList'
  generic 'hyperParams<-' and siglist 'MultiBatch,Hyperparameters'
  generic 'hyperParams<-' and siglist 'MultiBatchList,Hyperparameters'
  generic 'iter' and siglist 'McmcChains'
  generic 'iter' and siglist 'MultiBatch'
  generic 'iter' and siglist 'MultiBatchList'
  generic 'iter<-' and siglist 'McmcChains,ANY'
  generic 'iter<-' and siglist 'MultiBatch,numeric'
  generic 'iter<-' and siglist 'MultiBatchList,numeric'
  generic 'k' and siglist 'McmcChains'
  generic 'k' and siglist 'MultiBatch'
  generic 'k' and siglist 'MultiBatchList'
  generic 'k<-' and siglist 'McmcChains'
  generic 'label_switch' and siglist 'MultiBatch'
  generic 'length' and siglist 'MultiBatchList'
  generic 'logPrior' and siglist 'MultiBatch'
  generic 'log_lik' and siglist 'MultiBatch'
  generic 'marginal_lik' and siglist 'MultiBatch'
  generic 'marginal_lik' and siglist 'MultiBatchList'
  generic 'marginal_lik<-' and siglist 'MultiBatch,numeric'
  generic 'mcmcParams' and siglist 'MultiBatch'
  generic 'mcmcParams' and siglist 'MultiBatchList'
  generic 'mcmcParams<-' and siglist 'MultiBatch,McmcParams'
  generic 'mcmcParams<-' and siglist 'MultiBatchList,McmcParams'
  generic 'modelName' and siglist 'MultiBatch'
  generic 'modelName' and siglist 'MultiBatchList'
  generic 'modes' and siglist 'MultiBatch'
  generic 'modes' and siglist 'MultiBatchList'
  generic 'modes<-' and siglist 'MultiBatch'
  generic 'mu' and siglist 'MultiBatch'
  generic 'nStarts' and siglist 'MultiBatch'
  generic 'nStarts' and siglist 'MultiBatchList'
  generic 'nStarts<-' and siglist 'MultiBatch,integer'
  generic 'nStarts<-' and siglist 'MultiBatch,numeric'
  generic 'nStarts<-' and siglist 'MultiBatchList,integer'
  generic 'nStarts<-' and siglist 'MultiBatchList,numeric'
  generic 'names' and siglist 'MultiBatchList'
  generic 'nu.0' and siglist 'MultiBatch'
  generic 'oned' and siglist 'MultiBatch'
  generic 'oned' and siglist 'MultiBatchList'
  generic 'p' and siglist 'McmcChains'
  generic 'p' and siglist 'MultiBatch'
  generic 'posteriorSimulation' and siglist 'MultiBatch'
  generic 'posteriorSimulation' and siglist 'MultiBatchList'
  generic 'posteriorSimulation' and siglist 'MultiBatchP'
  generic 'posteriorSimulation' and siglist 'list'
  generic 'probz' and siglist 'MultiBatch'
  generic 'sigma2.0' and siglist 'MultiBatch'
  generic 'sigma2' and siglist 'MultiBatch'
  generic 'sigma' and siglist 'MultiBatchPooled'
  generic 'sigma<-' and siglist 'MixtureModel'
  generic 'sigma<-' and siglist 'MultiBatchPooled'
  generic 'tau2' and siglist 'MultiBatch'
  generic 'theta' and siglist 'MultiBatch'
  generic 'theta<-' and siglist 'McmcChains,ANY'
  generic 'theta<-' and siglist 'MixtureModel,ANY'
  generic 'theta<-' and siglist 'MultiBatch,matrix'
  generic 'theta<-' and siglist 'MultiBatchModel,ANY'
  generic 'thin' and siglist 'MultiBatch'
  generic 'thin' and siglist 'MultiBatchList'
  generic 'thin<-' and siglist 'McmcParams,numeric'
  generic 'thin<-' and siglist 'MultiBatch,numeric'
  generic 'thin<-' and siglist 'MultiBatchList,numeric'
  generic 'triodata_lrr' and siglist 'TrioBatchModel'
  generic 'z' and siglist 'MultiBatch'
  generic 'zFreq' and siglist 'MultiBatch'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
S4 class codoc mismatches from documentation object 'MixtureModel-class':
Slots for class 'MixtureModel'
  Code: .internal.constraint .internal.counter batch batchElements data
        data.mean data.prec hyperparams k label_switch loglik logprior
        marginal_lik mcmc.chains mcmc.params modes mu nu.0 pi
        predictive probz sigma2 sigma2.0 tau2 theta u z zfreq zstar
  Docs: .internal.constraint .internal.counter batch batchElements data
        data.mean data.prec hyperparams k label_switch loglik logprior
        marginal_lik marginal_lik mcmc.chains mcmc.params modes mu nu.0
        pi probz sigma2 sigma2.0 tau2 theta u z zfreq

S4 class codoc mismatches from documentation object 'MultiBatch-class':
Slots for class 'MultiBatch'
  Code: chains current_values data down_sample flags parameters specs
        summaries
  Docs: chains current_values data down_sample flags parameters
        summaries

S4 class codoc mismatches from documentation object 'MultiBatchModel-class':
Slots for class 'MultiBatchModel'
  Code: .internal.constraint .internal.counter batch batchElements data
        data.mean data.prec hyperparams k label_switch loglik logprior
        marginal_lik mcmc.chains mcmc.params modes mu nu.0 pi
        predictive probz sigma2 sigma2.0 tau2 theta u z zfreq zstar
  Inherited: k hyperparams theta sigma2 nu.0 sigma2.0 pi mu tau2
        predictive zstar data data.mean data.prec z zfreq probz u
        logprior loglik mcmc.chains batch batchElements modes
        mcmc.params label_switch marginal_lik .internal.constraint
        .internal.counter
  Docs: .internal.constraint batch batchElements data data.mean
        data.prec hyperparams is_mendelian k label_switch loglik
        logprior mcmc.chains mcmc.params modes mu nu.0 pi probz sigma2
        sigma2.0 tau2 theta z zfreq

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'HyperparametersTrios'
  'k' 'mu.0' 'tau2.0' 'eta.0' 'm2.0' 'alpha' 'beta' 'a' 'b' 'dfr'

Undocumented arguments in documentation object 'McmcParams'
  'min_GR' 'min_effsize' 'max_burnin' 'min_chains'

Duplicated \argument entries in documentation object 'MultiBatchModel2':
  'dat' 'batches' 'hp' 'mp'

Undocumented arguments in documentation object 'TrioBatchModel'
  'mprob' 'maplabel'
Documented arguments not in \usage in documentation object 'TrioBatchModel':
  'batches'

Undocumented arguments in documentation object 'gibbs'
  'maplabel' 'mprob'

Documented arguments not in \usage in documentation object 'iter<-':
  'force'

Documented arguments not in \usage in documentation object 'mcmcParams':
  'force'

Undocumented arguments in documentation object 'sigma<-'
  'value'

Undocumented arguments in documentation object 'singleBatchGuided,MultiBatchList,MultiBatch-method'
  'x' 'guide'

Undocumented arguments in documentation object 'theta'
  'value'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/CNPBayes/libs/i386/CNPBayes.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/CNPBayes/libs/x64/CNPBayes.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
MultiBatchModel  120.64   0.28  120.96
ggplot-functions  48.01   0.78   48.81
MBP               14.71   0.29   15.05
gibbs             11.83   0.08   11.91
upSample2          7.32   0.04    7.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
MultiBatchModel  65.25   0.08   65.36
ggplot-functions 43.42   0.06   43.50
MBP              14.80   0.07   14.90
gibbs            10.11   0.00   10.11
upSample2         5.42   0.07    5.50
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/CNPBayes.Rcheck/00check.log'
for details.



Installation output

CNPBayes.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/CNPBayes_1.13.5.tar.gz && rm -rf CNPBayes.buildbin-libdir && mkdir CNPBayes.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNPBayes.buildbin-libdir CNPBayes_1.13.5.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL CNPBayes_1.13.5.zip && rm CNPBayes_1.13.5.tar.gz CNPBayes_1.13.5.zip
###
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                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  893k  100  893k    0     0  14.0M      0 --:--:-- --:--:-- --:--:-- 15.8M

install for i386

* installing *source* package 'CNPBayes' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c miscfunctions.cpp -o miscfunctions.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c multibatch.cpp -o multibatch.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c multibatch_pooledvar.cpp -o multibatch_pooledvar.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c multibatch_reduced.cpp -o multibatch_reduced.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pooledvar_reduced.cpp -o pooledvar_reduced.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c triomodel.cpp -o triomodel.o
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o CNPBayes.dll tmp.def RcppExports.o miscfunctions.o multibatch.o multibatch_pooledvar.o multibatch_reduced.o pooledvar_reduced.o triomodel.o -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/CNPBayes.buildbin-libdir/CNPBayes/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'alpha' in package 'CNPBayes'
in method for 'convergence' with signature '"MultiBatchList"': no definition for class "MultiBatchList"
Creating a generic function from function 'sigma' in package 'CNPBayes'
Note: wrong number of arguments to '/' 
** help
*** installing help indices
  converting help for package 'CNPBayes'
    finding HTML links ... done
    BatchModelExample                       html  
    CNPBayes                                html  
    CopyNumber-classes                      html  
    CopyNumber-methods                      html  
    Defunct-classes                         html  
    Hyperparameters-class                   html  
    Hyperparameters                         html  
    HyperparametersBatch-class              html  
    HyperparametersMarginal-class           html  
    HyperparametersMultiBatch-class         html  
    HyperparametersMultiBatch               html  
    HyperparametersSingleBatch-class        html  
    HyperparametersSingleBatch              html  
    HyperparametersTrios-class              html  
    HyperparametersTrios                    html  
    MBP                                     html  
    MarginalModelExample                    html  
    McmcChains-class                        html  
    McmcParams-class                        html  
    McmcParams                              html  
    MixtureModel-class                      html  
    MultiBatch-class                        html  
    MultiBatchModel-class                   html  
    MultiBatchModel                         html  
    MultiBatchModelExample                  html  
    MultiBatchPooledExample                 html  
    SingleBatchModel-class                  html  
    SingleBatchModel                        html  
    SingleBatchModelExample                 html  
    TrioBatchModel                          html  
    bafLikelihood                           html  
    batch-method                            html  
    bayesFactor                             html  
    bic-method                              html  
    burnin-method                           html  
    chains-method                           html  
    chromosome                              html  
    collapseBatch-method                    html  
    consensusCNP                            html  
    copyNumber                              html  
    dfr-method                              html  
    downSample                              html  
    eta.0-method                            html  
    extract-methods                         html  
    findSurrogates-MultiBatch-method        html  
    ggplot-functions                        html  
    gibbs                                   html  
    hyperParams-method                      html  
    iter-method                             html  
    k-method                                html  
    label_switch                            html  
    logBayesFactor                          html  
    logPrior-method                         html  
    log_lik-method                          html  
    m2.0-method                             html  
    mapCnProbability                        html  
    mapParams                               html  
    map_z                                   html  
    mapping                                 html  
    marginalLik                             html  
    marginalLikelihood-method               html  
    marginal_lik                            html  
    mcmcParams-method                       html  
    mlParams                                html  
    modelName-MixtureModel-method           html  
    modes-method                            html  
    mu-method                               html  
    muMean                                  html  
    muc                                     html  
    nStarts-method                          html  
    names-methods                           html  
    nu.0-method                             html  
    numberObs-method                        html  
    oned-method                             html  
    orderModels                             html  
    p-MixtureModel-method                   html  
    pic                                     html  
    posteriorPredictive                     html  
    posteriorSimulation-method              html  
    posterior_cases                         html  
    pp                                      html  
    probCopyNumber                          html  
    probz-method                            html  
    probzpar-method                         html  
    qInverseTau2                            html  
    saveBatch                               html  
    sigma                                   html  
    sigma2-method                           html  
    sigma2.0-method                         html  
    sigmac                                  html  
    simulateBatchData                       html  
    simulateData                            html  
    singleBatchGuided-MultiBatchList-MultiBatch-method
                                            html  
    tau                                     html  
    tau2-method                             html  
    tauMean                                 html  
    tauc                                    html  
    theta-method                            html  
    thin-method                             html  
    tile-functions                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpIFAfHZ/R.INSTALL1f145fdc4500/CNPBayes/man/tile-functions.Rd:28: file link 'ntile' in package 'dplyr' does not exist and so has been treated as a topic
    triodata_lrr-method                     html  
    upSample2                               html  
    y-method                                html  
    z-method                                html  
    zfreq-method                            html  
    zfreqpar-method                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CNPBayes' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c miscfunctions.cpp -o miscfunctions.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c multibatch.cpp -o multibatch.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c multibatch_pooledvar.cpp -o multibatch_pooledvar.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c multibatch_reduced.cpp -o multibatch_reduced.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pooledvar_reduced.cpp -o pooledvar_reduced.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c triomodel.cpp -o triomodel.o
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o CNPBayes.dll tmp.def RcppExports.o miscfunctions.o multibatch.o multibatch_pooledvar.o multibatch_reduced.o pooledvar_reduced.o triomodel.o -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/CNPBayes.buildbin-libdir/CNPBayes/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNPBayes' as CNPBayes_1.13.5.zip
* DONE (CNPBayes)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'CNPBayes' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

CNPBayes.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2018-11-18 r75627) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.setenv("R_TESTS"="")
> library(testthat)
> library(CNPBayes)
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb

Attaching package: 'CNPBayes'

The following object is masked from 'package:stats':

    sigma

> test_check("CNPBayes")
== testthat results  ===========================================================
OK: 312 SKIPPED: 3 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 596.03    3.25  601.79 

CNPBayes.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2018-11-18 r75627) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> Sys.setenv("R_TESTS"="")
> library(testthat)
> library(CNPBayes)
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb

Attaching package: 'CNPBayes'

The following object is masked from 'package:stats':

    sigma

> test_check("CNPBayes")
== testthat results  ===========================================================
OK: 312 SKIPPED: 3 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 517.34    0.79  518.21 

Example timings

CNPBayes.Rcheck/examples_i386/CNPBayes-Ex.timings

nameusersystemelapsed
CopyNumber-methods000
Hyperparameters0.020.000.02
HyperparametersMultiBatch000
HyperparametersSingleBatch0.020.000.01
HyperparametersTrios000
MBP14.71 0.2915.05
McmcParams-class0.020.000.01
McmcParams000
MultiBatchModel120.64 0.28120.96
SingleBatchModel0.520.000.51
batch-method000
bic-method1.150.001.16
burnin-method000
chains-method000
chromosome0.030.000.04
collapseBatch-method0.490.000.48
consensusCNP0.220.000.21
copyNumber0.020.000.02
dfr-method000
downSample0.080.000.08
eta.0-method000
ggplot-functions48.01 0.7848.81
gibbs11.83 0.0811.91
hyperParams-method000
iter-method000
k-method0.070.000.08
label_switch000
logPrior-method000
log_lik-method000
m2.0-method000
mapParams000
map_z000
mapping000
marginalLikelihood-method1.380.001.39
marginal_lik000
mcmcParams-method000
mlParams000
modelName-MixtureModel-method000
modes-method000
mu-method000
muMean000
muc0.010.000.02
nStarts-method000
nu.0-method000
numberObs-method000
p-MixtureModel-method000
pic000
posteriorPredictive000
posteriorSimulation-method0.080.000.07
posterior_cases000
pp000
probz-method000
probzpar-method000
qInverseTau20.020.000.02
sigma000
sigma2-method000
sigma2.0-method000
sigmac0.000.020.02
simulateBatchData4.70.04.7
simulateData3.760.003.77
tau000
tau2-method0.030.000.03
tauMean000
tauc0.020.000.02
theta-method000
thin-method000
triodata_lrr-method000
upSample27.320.047.36
y-method000
z-method000
zfreq-method000
zfreqpar-method000

CNPBayes.Rcheck/examples_x64/CNPBayes-Ex.timings

nameusersystemelapsed
CopyNumber-methods0.010.000.02
Hyperparameters000
HyperparametersMultiBatch000
HyperparametersSingleBatch000
HyperparametersTrios000
MBP14.80 0.0714.90
McmcParams-class000
McmcParams0.010.000.02
MultiBatchModel65.25 0.0865.36
SingleBatchModel0.320.000.31
batch-method000
bic-method0.870.000.87
burnin-method000
chains-method0.020.000.02
chromosome0.030.000.03
collapseBatch-method0.400.000.41
consensusCNP0.180.000.17
copyNumber000
dfr-method000
downSample0.060.000.06
eta.0-method000
ggplot-functions43.42 0.0643.50
gibbs10.11 0.0010.11
hyperParams-method000
iter-method000
k-method0.120.000.13
label_switch000
logPrior-method000
log_lik-method000
m2.0-method000
mapParams000
map_z000
mapping000
marginalLikelihood-method1.020.001.05
marginal_lik000
mcmcParams-method000
mlParams000
modelName-MixtureModel-method000
modes-method000
mu-method000
muMean000
muc000
nStarts-method000
nu.0-method000
numberObs-method000
p-MixtureModel-method000
pic000
posteriorPredictive000
posteriorSimulation-method0.060.000.07
posterior_cases000
pp000
probz-method000
probzpar-method000
qInverseTau2000
sigma000
sigma2-method000
sigma2.0-method000
sigmac0.000.020.01
simulateBatchData4.310.004.31
simulateData2.770.002.77
tau000
tau2-method0.010.000.02
tauMean000
tauc000
theta-method000
thin-method0.010.000.02
triodata_lrr-method000
upSample25.420.075.50
y-method000
z-method000
zfreq-method000
zfreqpar-method000